Probing Nonadiabaticity of Proton-Coupled Electron Transfer in Ribonucleotide Reductase.

The enzyme ribonucleotide reductase, which is essential for DNA synthesis, initiates the conversion of ribonucleotides to deoxyribonucleotides via radical transfer over a 32 Å pathway composed of proton-coupled electron transfer (PCET) reactions. Previously, the first three PCET reactions in the α subunit were investigated with hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations. Herein, the fourth PCET reaction in this subunit between C439 and guanosine diphosphate (GDP) is simulated and found to be slightly exoergic with a relatively high free energy barrier. To further elucidate the mechanisms of all four PCET reactions, we analyzed the vibronic and electron-proton nonadiabaticities. This analysis suggests that interfacial PCET between Y356 and Y731 is vibronically and electronically nonadiabatic, whereas PCET between Y731 and Y730 and between C439 and GDP is fully adiabatic and PCET between Y730 and C439 is in the intermediate regime. These insights provide guidance for selecting suitable rate constant expressions for these PCET reactions.

A molecular-level mechanistic framework for interfacial proton-coupled electron transfer kinetics.

Electrochemical proton-coupled electron transfer (PCET) reactions can proceed via an outer-sphere electron transfer to solution (OS-PCET) or through an inner-sphere mechanism by interfacial polarization of surface-bound active sites (I-PCET). Although OS-PCET has been extensively studied with molecular insight, the inherent heterogeneity of surfaces impedes molecular-level understanding of I-PCET. Herein we employ graphite-conjugated carboxylic acids (GC-COOH) as molecularly well-defined hosts of I-PCET to isolate the intrinsic kinetics of I-PCET. We measure I-PCET rates across the entire pH range, uncovering a V-shaped pH-dependence that lacks the pH-independent regions characteristic of OS-PCET. Accordingly, we develop a mechanistic model for I-PCET that invokes concerted PCET involving hydronium/water or water/hydroxide donor/acceptor pairs, capturing the entire dataset with only four adjustable parameters. We find that I-PCET is fourfold faster with hydronium/water than water/hydroxide, while both reactions display similarly high charge transfer coefficients, indicating late proton transfer transition states. These studies highlight the key mechanistic distinctions between I-PCET and OS-PCET, providing a framework for understanding and modelling more complex multistep I-PCET reactions critical to energy conversion and catalysis.

Direct Evidence for a Sequential Electron Transfer-Proton Transfer Mechanism in the PCET Reduction of a Metal Hydroxide Catalyst.

The proton-coupled electron transfer (PCET) mechanism for the reaction Mox-OH + e- + H+ → Mred-OH2 was determined through the kinetic resolution of the independent electron transfer (ET) and proton transfer (PT) steps. The reaction of interest was triggered by visible light excitation of [RuII(tpy)(bpy')H2O]2+, RuII-OH2, where tpy is 2,2':6',2″-terpyridine and bpy' is 4,4'-diaminopropylsilatrane-2,2'-bipyridine, anchored to In2O3:Sn (ITO) thin films in aqueous solutions. Interfacial kinetics for the PCET reduction reaction were quantified by nanosecond transient absorption spectroscopy as a function of solution pH and applied potential. Data acquired at pH = 5-10 revealed a stepwise electron transfer-proton transfer (ET-PT) mechanism, while kinetic measurements made below pKa(RuIII-OH/OH2) = 1.3 were used to study the analogous interfacial reaction, where electron transfer was the only mechanistic step. Analysis of this data with a recently reported multichannel kinetic model was used to construct a PCET zone diagram and supported the assignment of an ET-PT mechanism at pH = 5-10. Ultimately, this study represents a unique example among Mox-OH/Mred-OH2 reactivity where the protonation and oxidation states of the intermediate were kinetically and spectrally resolved to firmly establish the PCET mechanism.

Modeling the Weak pH Dependence of Proton-Coupled Electron Transfer for Tryptophan Derivatives.

The oxidation of tryptophan (Trp) is an important step in many biological processes and often occurs by sequential or concerted proton-coupled electron transfer (PCET). The apparent rate constants for the photochemical oxidation of two Trp derivatives in water have been shown to be pH-independent at low pH and to exhibit weak pH dependence at higher pH. Herein, these systems are investigated with a general, multi-channel model that includes sequential and concerted mechanisms as well as various proton donors and acceptors. This model can reproduce the kinetic data for both Trp derivatives with physically meaningful parameters and suggests that the weak pH dependence may arise from the competition between OH- and H2O as proton acceptors in concerted PCET. Deprotonation of an ammonium group for one of the systems leads to a more complex pH dependence at higher pH. This work demonstrates the importance of considering multiple competing channels for the analysis of the pH dependence of apparent PCET rate constants.

General Kinetic Model for pH Dependence of Proton-Coupled Electron Transfer: Application to an Electrochemical Water Oxidation System.

The pH dependence of proton-coupled electron transfer (PCET) reactions, which are critical to many chemical and biological processes, is a powerful probe for elucidating their fundamental mechanisms. Herein, a general, multichannel kinetic model is introduced to describe the pH dependence of both homogeneous and electrochemical PCET reactions. According to this model, a weak pH dependence can arise from the competition among multiple sequential and concerted PCET channels involving different forms of the redox species, such as protonated and deprotonated forms, as well as different proton donors and acceptors. The contribution of each channel is influenced by the relative populations of the reactant species, which often depend strongly on pH, leading to complex pH dependence of PCET apparent rate constants. This model is used to explain the origins of the experimentally observed weak pH dependence of the electrochemical PCET apparent rate constant for a ruthenium-based water oxidation catalyst attached to a tin-doped In2O3 (ITO) surface. The weak pH dependence is found to arise from the intrinsic differences in the rate constants of participating channels and the dependence of their relative contributions on pH. This model predicts that the apparent maximum rate constant will become pH-independent at higher pH, which is confirmed by experimental measurements. Our analysis also suggests that the dominant channels are electron transfer at lower pH and sequential PCET via electron transfer followed by fast proton transfer at higher pH. This work highlights the importance of considering multiple competing channels simultaneously for PCET processes.

Computational Insights into the Mechanism of Nitric Oxide Generation from S-Nitrosoglutathione Catalyzed by a Copper Metal-Organic Framework.

The controlled generation of nitric oxide (NO) from endogenous sources, such as S-nitrosoglutathione (GSNO), has significant implications for biomedical implants due to the vasodilatory and other beneficial properties of NO. The water-stable metal-organic framework (MOF) Cu-1,3,5-tris[1H-1,2,3-triazol-5-yl]benzene has been shown to catalyze the production of NO and glutathione disulfide (GSSG) from GSNO in aqueous solution as well as in blood. Previous experimental work provided kinetic data for the catalysis of the 2GSNO → 2NO + GSSG reaction, leading to various proposed mechanisms. Herein, this catalytic process is examined using density functional theory. Minimal functional models of the Cu-MOF cluster and glutathione moieties are established, and three distinct catalytic mechanisms are explored. The most thermodynamically favorable mechanism studied is consistent with prior experimental findings. This mechanism involves coordination of GSNO to copper via sulfur rather than nitrogen and requires a reductive elimination that produces a Cu(I) intermediate, implicating a redox-active copper site. The experimentally observed inhibition of reactivity at high pH values is explained in terms of deprotonation of a triazole linker, which decreases the structural stability of the Cu(I) intermediate. These fundamental mechanistic insights may be generally applicable to other MOF catalysts for NO generation.

Design of an Electrostatic Frequency Map for the NH Stretch of the Protein Backbone and Application to Chiral Sum Frequency Generation Spectroscopy.

We develop an electrostatic map for the vibrational NH stretch (amide A) of the protein backbone with a focus on vibrational chiral sum frequency generation spectroscopy (chiral SFG). Chiral SFG has been used to characterize protein secondary structure at interfaces using the NH stretch and to investigate chiral water superstructures around proteins using the OH stretch. Interpretation of spectra has been complicated because the NH stretch and OH stretch overlap spectrally. Although an electrostatic map for water OH developed by Skinner and co-workers was used previously to calculate the chiral SFG response of water structures around proteins, a map for protein NH that is directly responsive to biological complexity has yet to be developed. Here, we develop such a map, linking the local electric field to vibrational frequencies and transition dipoles. We apply the map to two protein systems and achieve much better agreement with experiment than was possible in our previous studies. We show that couplings between NH and OH vibrations are crucial to the line shape, which informs the interpretation of chiral SFG spectra, and that the chiral NH stretch response is sensitive to small differences in structure. This work increases the utility of the NH stretch in biomolecular spectroscopy.

Inverse kinetic isotope effects in the oxygen reduction reaction at platinum single crystals.

Although the oxygen reduction reaction (ORR) involves multiple proton-coupled electron transfer processes, early studies reported the absence of kinetic isotope effects (KIEs) on polycrystalline platinum, probably due to the use of unpurified D2O. Here we developed a methodology to prepare ultra-pure D2O, which is indispensable for reliably investigating extremely surface-sensitive platinum single crystals. We find that Pt(111) exhibits much higher ORR activity in D2O than in H2O, with potential-dependent inverse KIEs of ~0.5, whereas Pt(100) and Pt(110) exhibit potential-independent inverse KIEs of ~0.8. Such inverse KIEs are closely correlated to the lower *OD coverage and weakened *OD binding strength relative to *OH, which, based on theoretical calculations, are attributed to the differences in their zero-point energies. This study suggests that the competing adsorption between *OH/*OD and *O2 probably plays an important role in the ORR rate-determining steps that involve a chemical step preceding an electrochemical step (CE mechanism).

Reorganization Energies for Interfacial Proton-Coupled Electron Transfer to a Water Oxidation Catalyst.

The reorganization energy (λ) for interfacial electron transfer (ET) and proton-coupled ET (PCET) from a conductive metal oxide (In2O3:Sn, ITO) to a surface-bound water oxidation catalyst was extracted from kinetic data measured as a function of the thermodynamic driving force. Visible light excitation resulted in rapid excited-state injection (kinj > 108 s-1) to the ITO, which photo-initiated the two interfacial reactions of interest. The rate constants for both reactions increased with the driving force, -ΔG°, to a saturating limit, kmax, with rate constants consistently larger for ET than for PCET. Marcus-Gerischer analysis of the kinetic data provided the reorganization energy for interfacial PCET (0.90 ± 0.02 eV) and ET (0.40 ± 0.02 eV), respectively. The magnitude of kmax for PCET was found to decrease with pH, behavior that was absent for ET. Both the decrease in kmax and the larger reorganization energy for an unwanted competing PCET reaction from the ITO to the oxidized catalyst showcases a significant kinetic advantage for driving solar water oxidation at high pH. Computational analysis revealed a larger inner-sphere reorganization energy contribution for PCET than for ET arising from a more significant change in the Ru-O bond length for the PCET reaction. Extending the Marcus-Gerischer theory to PCET by including the excited electron-proton vibronic states and the proton donor-acceptor motion provided an apparent reorganization energy of 1.01 eV. This study demonstrates that the Marcus-Gerischer theory initially developed for ET can be reliably extended to PCET for quantifying and interpreting reorganization energies observed experimentally.

Kinetic model for reversible radical transfer in ribonucleotide reductase.

The enzyme ribonucleotide reductase (RNR), which catalyzes the reduction of ribonucleotides to deoxynucleotides, is vital for DNA synthesis, replication, and repair in all living organisms. Its mechanism requires long-range radical translocation over ∼32 Šthrough two protein subunits and the intervening aqueous interface. Herein, a kinetic model is designed to describe reversible radical transfer in Escherichia coli RNR. This model is based on experimentally studied photoRNR systems that allow the photochemical injection of a radical at a specific tyrosine residue, Y356, using a photosensitizer. The radical then transfers across the interface to another tyrosine residue, Y731, and continues until it reaches a cysteine residue, C439, which is primed for catalysis. This kinetic model includes radical injection, an off-pathway sink, radical transfer between pairs of residues along the pathway, and the conformational flipping motion of Y731 at the interface. Most of the input rate constants for this kinetic model are obtained from previous experimental measurements and quantum mechanical/molecular mechanical free-energy simulations. Ranges for the rate constants corresponding to radical transfer across the interface are determined by fitting to the experimentally measured Y356 radical decay times in photoRNR systems. This kinetic model illuminates the time evolution of radical transport along the tyrosine and cysteine residues following radical injection. Further analysis identifies the individual rate constants that may be tuned to alter the timescale and probability of the injected radical reaching C439. The insights gained from this kinetic model are relevant to biochemical understanding and protein-engineering efforts with potential pharmacological implications.

Theoretical Modeling of Electrochemical Proton-Coupled Electron Transfer.

Proton-coupled electron transfer (PCET) plays an essential role in a wide range of electrocatalytic processes. A vast array of theoretical and computational methods have been developed to study electrochemical PCET. These methods can be used to calculate redox potentials and pKa values for molecular electrocatalysts, proton-coupled redox potentials and bond dissociation free energies for PCET at metal and semiconductor interfaces, and reorganization energies associated with electrochemical PCET. Periodic density functional theory can also be used to compute PCET activation energies and perform molecular dynamics simulations of electrochemical interfaces. Various approaches for maintaining a constant electrode potential in electronic structure calculations and modeling complex interactions in the electric double layer (EDL) have been developed. Theoretical formulations for both homogeneous and heterogeneous electrochemical PCET spanning the adiabatic, nonadiabatic, and solvent-controlled regimes have been developed and provide analytical expressions for the rate constants and current densities as functions of applied potential. The quantum mechanical treatment of the proton and inclusion of excited vibronic states have been shown to be critical for describing experimental data, such as Tafel slopes and potential-dependent kinetic isotope effects. The calculated rate constants can be used as input to microkinetic models and voltammogram simulations to elucidate complex electrocatalytic processes.

Electrocatalysis in Alkaline Media and Alkaline Membrane-Based Energy Technologies.

Hydrogen energy-based electrochemical energy conversion technologies offer the promise of enabling a transition of the global energy landscape from fossil fuels to renewable energy. Here, we present a comprehensive review of the fundamentals of electrocatalysis in alkaline media and applications in alkaline-based energy technologies, particularly alkaline fuel cells and water electrolyzers. Anion exchange (alkaline) membrane fuel cells (AEMFCs) enable the use of nonprecious electrocatalysts for the sluggish oxygen reduction reaction (ORR), relative to proton exchange membrane fuel cells (PEMFCs), which require Pt-based electrocatalysts. However, the hydrogen oxidation reaction (HOR) kinetics is significantly slower in alkaline media than in acidic media. Understanding these phenomena requires applying theoretical and experimental methods to unravel molecular-level thermodynamics and kinetics of hydrogen and oxygen electrocatalysis and, particularly, the proton-coupled electron transfer (PCET) process that takes place in a proton-deficient alkaline media. Extensive electrochemical and spectroscopic studies, on single-crystal Pt and metal oxides, have contributed to the development of activity descriptors, as well as the identification of the nature of active sites, and the rate-determining steps of the HOR and ORR. Among these, the structure and reactivity of interfacial water serve as key potential and pH-dependent kinetic factors that are helping elucidate the origins of the HOR and ORR activity differences in acids and bases. Additionally, deliberately modulating and controlling catalyst-support interactions have provided valuable insights for enhancing catalyst accessibility and durability during operation. The design and synthesis of highly conductive and durable alkaline membranes/ionomers have enabled AEMFCs to reach initial performance metrics equal to or higher than those of PEMFCs. We emphasize the importance of using membrane electrode assemblies (MEAs) to integrate the often separately pursued/optimized electrocatalyst/support and membranes/ionomer components. Operando/in situ methods, at multiscales, and ab initio simulations provide a mechanistic understanding of electron, ion, and mass transport at catalyst/ionomer/membrane interfaces and the necessary guidance to achieve fuel cell operation in air over thousands of hours. We hope that this Review will serve as a roadmap for advancing the scientific understanding of the fundamental factors governing electrochemical energy conversion in alkaline media with the ultimate goal of achieving ultralow Pt or precious-metal-free high-performance and durable alkaline fuel cells and related technologies.

Investigation of the pKa of the Nucleophilic O2' of the Hairpin Ribozyme.

Small ribozymes cleave their RNA phosphodiester backbone by catalyzing a transphosphorylation reaction wherein a specific O2' functions as the nucleophile. While deprotonation of this alcohol through its acidification would increase its nucleophilicity, little is known about the pKa of this O2' in small ribozymes, in part because high pKa's are not readily accessible experimentally. Herein, we turn to molecular dynamics to calculate the pKa of the nucleophilic O2' in the hairpin ribozyme and to study interactions within the active site that may impact its value. We estimate the pKa of the nucleophilic O2' in the wild-type hairpin ribozyme to be 18.5 ± 0.8, which is higher than the reference compound, and identify a correlation between proper positioning of the O2' for nucleophilic attack and elevation of its pKa. We find that monovalent ions may play a role in depression of the O2' pKa, while the exocyclic amine appears to be important for organizing the ribozyme active site. Overall, this study suggests that the pKa of the O2' is raised in the ground state and lowers during the course of the reaction owing to positioning and metal ion interactions.

Artificial Neural Networks as Propagators in Quantum Dynamics.

The utilization of artificial neural networks (ANNs) provides strategies for accelerating molecular simulations. Herein, ANNs are implemented as propagators of the time-dependent Schrödinger equation to simulate the quantum dynamics of systems with time-dependent potentials. These ANN propagators are trained to map nonstationary wavepackets from a given time to a future time within the discrete variable representation. Each propagator is trained for a specified time step, and iterative application of the propagator enables the propagation of wavepackets over long time scales. Such ANN propagators are developed and applied to one- and two-dimensional proton transfer systems, which exhibit nuclear quantum effects such as hydrogen tunneling. These ANN propagators are trained for either a specific time-independent potential or general potentials that can be time-dependent. Hierarchical, multiple time step algorithms enable parallelization, and the extension to higher dimensions is straightforward. This strategy is applicable to quantum dynamical simulations of diverse chemical and biological processes.

Artificial Neural Networks as Mappings between Proton Potentials, Wave Functions, Densities, and Energy Levels.

Artificial neural networks (ANNs) have become important in quantum chemistry. Herein, applications to nuclear quantum effects, such as zero-point energy, vibrationally excited states, and hydrogen tunneling, are explored. ANNs are used to solve the time-independent Schrödinger equation for single- and double-well potentials representing hydrogen-bonded molecular systems capable of proton transfer. ANN mappings are trained to predict the lowest five proton vibrational energies, wave functions, and densities from the proton potentials and to predict the excited state proton vibrational energies and densities from the proton ground state density. For the inverse problem, ANN mappings are trained to predict the proton potential from the proton vibrational energy levels or the proton ground state density. This latter mapping is theoretically justified by the first Hohenberg-Kohn theorem establishing a one-to-one correspondence between the external potential and the ground state density. ANNs for two- and three-dimensional systems are also presented to illustrate the straightforward extension to higher dimensions.

Theoretical Description of the Primary Proton-Coupled Electron Transfer Reaction in the Cytochrome bc1 Complex.

The cytochrome bc1 complex is a transmembrane enzymatic protein complex that plays a central role in cellular energy production and is present in both photosynthetic and respiratory chain organelles. Its reaction mechanism is initiated by the binding of a quinol molecule to an active site, followed by a series of charge transfer reactions between the quinol and protein subunits. Previous work hypothesized that the primary reaction was a concerted proton-coupled electron transfer (PCET) reaction because of the apparent absence of intermediate states associated with single proton or electron transfer reactions. In the present study, the kinetics of the primary bc1 complex PCET reaction is investigated with a vibronically nonadiabatic PCET theory in conjunction with all-atom molecular dynamics simulations and electronic structure calculations. The computed rate constants and relatively high kinetic isotope effects are consistent with experimental measurements on related biomimetic systems. The analysis implicates a concerted PCET mechanism with significant hydrogen tunneling and nonadiabatic effects in the bc1 complex. Moreover, the employed theoretical framework is shown to serve as a general strategy for describing PCET reactions in bioenergetic systems.

Theoretical Study of Shallow Distance Dependence of Proton-Coupled Electron Transfer in Oligoproline Peptides.

Long-range electron transfer is coupled to proton transfer in a wide range of chemically and biologically important processes. Recently the proton-coupled electron transfer (PCET) rate constants for a series of biomimetic oligoproline peptides linking Ru(bpy)32+ to tyrosine were shown to exhibit a substantially shallower dependence on the number of proline spacers compared to the analogous electron transfer (ET) systems. The experiments implicated a concerted PCET mechanism involving intramolecular electron transfer from tyrosine to Ru(bpy)33+ and proton transfer from tyrosine to a hydrogen phosphate dianion. Herein these PCET systems, as well as the analogous ET systems, are studied with microsecond molecular dynamics, and the ET and PCET rate constants are calculated with the corresponding nonadiabatic theories. The molecular dynamics simulations illustrate that smaller ET donor-acceptor distances are sampled by the PCET systems than by the analogous ET systems. The shallower dependence of the PCET rate constant on the ET donor-acceptor distance is explained in terms of an additional positive, distance-dependent electrostatic term in the PCET driving force, which attenuates the rate constant at smaller distances. This electrostatic term depends on the change in the electrostatic interaction between the charges on each end of the bridge and can be modified by altering these charges. On the basis of these insights, this theory predicted a less shallow distance dependence of the PCET rate constant when imidazole rather than hydrogen phosphate serves as the proton acceptor, even though their pKa values are similar. This theoretical prediction was subsequently validated experimentally, illustrating that long-range electron transfer processes can be tuned by modifying the nature of the proton acceptor in concerted PCET processes. This level of control has broad implications for the design of more effective charge-transfer systems.

Kinetics of Proton Discharge on Metal Electrodes: Effects of Vibrational Nonadiabaticity and Solvent Dynamics.

Proton discharge on metal electrodes, also denoted the Volmer reaction, is a critical step in a wide range of electrochemical processes. This electrochemical proton-coupled electron transfer (PCET) reaction is predominantly electronically adiabatic in aqueous solution and is typically treated as fully adiabatic. Recently, a theoretical model for this PCET reaction was developed to generate the vibronic free energy surfaces as functions of a collective solvent coordinate and the distance of the proton-donating acid from the electrode. Herein a unified formulation is devised to describe such PCET reactions in terms of a curve crossing between two diabatic vibronic states corresponding to the lowest two proton vibrational states, employing an interpolation scheme that spans the adiabatic transition state theory, nonadiabatic Fermi golden rule, and solvent-controlled regimes. In contrast to previous treatments, application of this formulation to the aqueous Volmer reaction highlights the importance of vibrational nonadiabaticity and solvent dynamics. The calculated transfer coefficients and kinetic isotope effects are in reasonable agreement with experimental measurements. These fundamental insights have broad implications for understanding electrochemical processes.

Theoretical analysis of the inverted region in photoinduced proton-coupled electron transfer.

Photoinduced proton-coupled electron transfer (PCET) plays a key role in a wide range of energy conversion processes, and understanding how to design systems to control the PCET rate constant is a significant challenge. Herein a theoretical formulation of PCET is utilized to identify the conditions under which photoinduced PCET may exhibit inverted region behavior. In the inverted region, the rate constant decreases as the driving force increases even though the reaction becomes more thermodynamically favorable. Photoinduced PCET will exhibit inverted region behavior when the following criteria are satisfied: (1) the overlap integrals corresponding to the ground reactant and the excited product proton vibrational wavefunctions become negligible for a low enough product vibronic state and (2) the reaction free energies associated with the lower excited product proton vibrational wavefunctions contributing significantly to the rate constant are negative with magnitudes greater than the reorganization energy. These criteria are typically not satisfied by harmonic or Morse potentials but are satisfied by more realistic asymmetric double well potentials because the proton vibrational states above the barrier correspond to more delocalized proton vibrational wavefunctions with nodal structures leading to destructive interference effects. Thus, this theoretical analysis predicts that inverted region behavior could be observed for systems with asymmetric double well potentials characteristic of hydrogen-bonded systems and that the hydrogen/deuterium kinetic isotope effect will approach unity and could even become inverse in this region due to the oscillatory nature of the highly excited vibrational wavefunctions. These insights may help guide the design of more effective energy conversion devices.